I’m surprised it hasn’t been mentioned yet, but there’s the entirety of Full Metal Alchemist’s first TV Series that starts pretty close but ends up diverging significantly. Many people find the ending of this original anime to be a huge disappointment – to the point where they completely redid the anime.

Trigun manga and the original TV series diverged, but it’s really up to debate whether the TV show is “worse” as I really think the quality of the show is mostly good but starts to show rough edges on the occasional episode. The last episode is pretty fantastic though, so they stuck the landing IMO. I think the story of the most recent Trigun Stampede is quite a bit worse than both the manga and the original series, though I would say that even the manga made some of the same mistakes but in different ways if… that makes sense lol.

Also, and this is a bit of a cop-out, but many of the Leiji Matsumoto manga projects are adapted completely differently with each movie / series / book having a completely isolated but similar continuity. This is an intentional design and is even true with all of his individual manga works. I’s part of his “Rings of Time” system, which allows characters to exist across multiple continuities and timelines. Anyway, while most of these projects resulted in some of the greatest shows and movies of anime legacy, there are also notably a few duds so it’s always worth reading reviews of a specific series / run and see whether people recommend a different series if you are interested in the characters.